Matrix assisted laser desorption (MALD) coupled to time-of-flight mass spectrometry has emerged in recent years as a powerful resource for the biomedical researcher. Applications to the analysis of a wide range of important classes of biomolecules, including proteins, peptides, monoclonal antibodies, oligonucleotides and glycopeptides and glycoproteins have been particularly impressive. Basic studies of the fundamental mechanism involved in matrix assisted laser desorption are needed to gain an improved understanding of the desorption process itself. Such studies are expected to expand the applicability of the technique and provide improvements in such areas as molecular mass accuracy, sensitivity and mass resolution. A primary concern is the nature of the matrix/analyte interactions. For peptides and proteins, significant matrix adduct species are observed. The exact mechanism for formation of these species is not known, but involve simple dehydration and decarboxylation reactions. The net result are ion species which interfere with the accurate determination of a samples molecular weight, particularly for large mass analytes such as proteins. A variety of studies aimed at elucidating the nature of these matrix adduct species are described, with the goal of reducing or eliminating these troublesome reactions, thus improving the utility of the data available from this technique. Indeed, if this can be accomplished, it is probable that even more complicated biomolecular systems can be probed by this technique. Examples include binding studies of various small molecules (such as pharmaceuticals) to large proteins (more than 30,000 Da), which currently are difficult to perform with this technique. Instrumental methods are proposed to improve the performance of the MALD technique. These include utilizing an electrostatic sector from a conventional double sector mass spectrometer as an energy filter to improve the mass resolving power available. This will allow more detailed studies of the matrix adduct reactions as well as improving the utility for biomolecular studies. In order to increase the structural information available from the MALD experiment, surface induced dissociation studies are described for performing MS/MS experiments on the protonated molecular ions produced by MALD.